


Scientifically Compatible

by cozy_cinnamondrinks_and_starrynights



Series: Building A Family [1]
Category: Marvel Cinematic Universe
Genre: Actions has consequences, BAMF Laura Barton, BAMF Team Iron Man, Both of them loves Rhodey, Bruce comes back, Bucky gets help, Domestic Fluff, Extremis Tony Stark, F/F, Hurt Tony Stark, I REGRET NOTHING, I just wanted to write Science Bros and Rhodey with Bucky, James "Rhodey" Rhodes is a Good Bro, M/M, Natasha Romanov Is a Good Bro, Natasha plays matchmaker, New Avengers, Not A Fix-It, Not Avengers: Infinity War Part 1 (Movie) Compliant, Not Clint Friendly, Not Steve Friendly, People Loves Tony, Pepper Potts Is a Good Bro, Pepper plays matchmaker, Protective Bruce Banner, Protective James "Rhodey" Rhodes, Protective Pepper Potts, Stay At Home Husband Tony Stark, Stay At Home Parent Tony Stark, That lovely au where Natasha Stays, The Author Regrets Nothing, The Author is Salty about Civil War, Tony Stark Defense Squad, Tony Stark Has A Heart, Tony Stark Needs a Hug, Tony Stark is a Trophy Husband, Tony is quite popular with mutants, WarWinter, Winter Solider is a separate personality, Wintermachine?, gen z humor, not really - Freeform, not team Cap friendly, not wanda maximoff friendly
Language: English
Status: In-Progress
Published: 2018-12-09
Updated: 2018-12-30
Packaged: 2019-09-15 04:39:47
Rating: Not Rated
Warnings: Creator Chose Not To Use Archive Warnings
Chapters: 3
Words: 3,564
Publisher: archiveofourown.org
Story URL: https://archiveofourown.org/works/16926669
Author URL: https://archiveofourown.org/users/cozy_cinnamondrinks_and_starrynights/pseuds/cozy_cinnamondrinks_and_starrynights
Summary: “Thank you.” Bruce nods at her before turning back to Tony. “C-can I have a moment alone with Tony? Please?” Pepper watches him silently before nodding and leaving. Once she was gone, tears slip down Bruce’s face. “Oh gods, Tony I’m so sorry..” He begins to cry. “I’m sorry I wasn’t there for you and that I just left after the Ultron incident..but that witch..it made everything to much..” He says softly then chuckles. “That’s no excuse..though.” He gently takes Tony’s hand. “You’re the strongest avenger Tony..you’ve been pushed and beaten but you still made it through. No training, no enhancements..it was all purely you. Your genius, your technology..your willpower. It’s truly a sight to behold.” He sighs softly as he slowly opens his eyes not realizing he had closed them. He stares into tired brown eyes. “Tony..?”





	1. The Return

Bruce looks up at Stark Tower and sighs softly. He wonders if this was a good idea and if it was too late to turn back. He shakes his head. ‘No, I have to do this.’ He thinks to himself before walking inside. Inside, Pepper was talking to some employees when she spots Bruce. “Bruce Banner.” She greets politely. Bruce jumps slightly but turns to face her.

“Ms. Potts.” He nods at her fidgeting slightly. “U-uh can I speak to Tony? Uh- I mean Mr. Stark?” Bruce winces as Pepper’s face darken slightly.

“You may but I doubt he’ll be able to speak.” Pepper says shortly. Bruce looks at her in confusion. She motions for him to follow her and walks to the company’s car. They both got in and Pepper instructs Happy to the hospital. Bruce fidgets nervously.

“Uh. Ms. Potts? Why is Tony- Mr. Stark I mean, in the hospital?” He asks quietly. Pepper looks at him in disbelief before gaining a look of understanding.

“You haven’t heard of the accords or the ‘Civil War’ have you?” Pepper asks calmly. Bruce shakes his head and Pepper begins to explain what happened. Bruce listens and a sense of dread sat in chest as she spoke. Before Pepper could finish, they arrived at the hospital. They both got out and walks inside after thanking Happy. “Tony Stark please.” Pepper tells the receptionist who gives them a key to the room. They walk in silence to Tony’s room. Bruce’s eyes widen at the sight of Tony hooked up to machines.

“Wh-what happened..?” Bruce whispers in shock. Pepper frowns and points at the ground a bit away from Tony’s bed.

“That happened. Steve Rogers happened.” Pepper growls. Bruce looks at where she was pointing and looks on in shock at the shield on the ground.

“What did he do..” Bruce whispers as he stumbles into a seat.

“He slammed his shield into Tony’s chest. Multiple times.” Pepper says shortly.

“Isn’t that shield made of Vibranium..?” Bruce asks still in shock as to what had happened to his friend. Pepper nods. “Didn’t he know that could have killed Tony? What was he thinking? Why did he do that?!” Bruce asks gripping his chair.

“James Barnes.”

“Who?”

“James Barnes. He was Rogers’ friend in the 40’s. He fell from a train and was found by HYDRA. They brainwashed him and created the Winter Soldier. Once Rogers found out he started trying to find his friend and he did.” Bruce’s head was spinning from the information he was given.

“What does that do with Tony?” He asks quietly dreading the answer.

“The Winter Soldier killed Tony’s parents. Rogers knew for almost two years and didn’t tell him. He found out from a video in Siberia.”

“So he attacked James?”

“No, he attacked Rogers because he knew.”

“And Rogers hit him with the shield...in the chest..a normal person..against both Vibranium and superhuman strength.” Pepper nods and Bruce took a deep breath. “All because Rogers didn’t agree with the accords and for his friend..?” She nods again. “Can I see the accords?”

“I’ll give them to you once we return to Stark Tower.”

“Thank you.” Bruce nods at her before turning back to Tony. “C-can I have a moment alone with Tony? Please?” Pepper watches him silently before nodding and leaving. Once she was gone, tears slip down Bruce’s face. “Oh gods, Tony I’m so sorry..” He begins to cry. “I’m sorry I wasn’t there for you and that I just left after the Ultron incident..but that witch..it made everything to much..” He says softly then chuckles. “That’s no excuse..though.” He gently takes Tony’s hand. “You’re the strongest avenger Tony..you’ve been pushed and beaten but you still made it through. No training, no enhancements..it was all purely you. Your genius, your technology..your willpower. It’s truly a sight to behold.” He sighs softly as he slowly opens his eyes not realizing he had closed them. He stares into tired brown eyes. “Tony..?”

Tony smiles a bit. “H-hey Brucie Bear..” He says softly attempting to sit up only for Bruce to stop him.

“Stay down, you need your rest.” Bruce says firmly. Tony shakes his head.

“Bruce, I have work to do..”

“You need to recover.”

“Bruce..”

“Tony.” They stare at each other before Tony groan and lays back. “Thank you.”

“So, what got you to come back to New York?” Tony asks watching him.

“I-I wanted to apologize and rekindle our friendship. I’m so sorry that I left you alone after the Ultron incident-” Tony waves him off.

“I heard your speech..I..I can’t say I forgive you..yet..” Tony hesitates looking at Bruce. Bruce nods in understanding. “But I’m sure we can work out something..” Tony smiles brightly making Bruce smile back.

“Yeah, I’ll make sure to visit you. I’m going to talk to Ms. Potts about the Accords. I’m here for you Tony..and..I’m not going to leave you again..” Bruce promises but Tony has already fallen asleep. Bruce walks out of the room quietly and looks at Pepper. “So..the Accords?” Bruce asks.

“Of course, please follow me.”


	2. Extremis

**Summary for the Chapter:**

> Rhodey speaks to Bruce, Tony gets Extremis, and A suggestion

Bruce paces in the waiting room after Tony had been taken in for surgery. He still couldn’t wrap his head around the fact that Steve, _Captain America_ , beat a non-enhanced human, a civilian at that, with his vibranium shield. If that wasn’t enough, he left him! Left a baseline human in Siberia with no way of knowing if he would survive or not. All for his friend, James Barnes. There was a hint of green around his irises but he takes some calming breaths as Pepper arrives. He looks at her in hopes she had good news.

“There is only one way we can make sure Tony lives.” Pepper says quietly before taking a breath. “It’s called Extremis, Tony told me to use it as a last resort.. The doctors are saying that he might not make it and I-” Bruce remains silent as he thinks this over. Obviously Tony was okay with it but he has quite a bit of a problem with what he’s okay with.

“What will it do?” Bruce finally got up the courage to ask.

“It will heal him all the way through, all the damage done to his body would be completely reverse. He’ll be completely healthy...physically.” Pepper adds on the last part for emphasis. Bruce sighs as he thinks before nodding.

“Alright, we should do it then..” Bruce concedes. Pepper nods and walks off.

The doctors began injecting Tony with Extremis while Bruce was intercepted by James ‘Rhodey’ Rhodes aka War Machine and Tony’s Best Friend. “Dr. Banner.” He greets neutrally.

“Colonel Rhodes.” Bruce greets the man respectfully.

“Glad to see you’re back from...wherever you hide yourself.” He narrows his eyes at him. Bruce fidgets nervously.

“Yeah..I’m sorry..”

“You shouldn’t be apologizing to me.”

“I apologized to Tony already.” Rhodey looks at Bruce then tilts his head his eyes calculative.

"Did he forgive you?”

“No, he said we can work something out but he wouldn’t forgive me yet.. I honestly don’t blame him for not forgiving me.” There was a self-depreciative smile on the doctor’s face. “He was the first one to accept me, no us, both the Hulk and I with no fear. He didn’t ignore him like the rest of us did.. Then I just up and leave him because of that _stupid witch_.” Rhodey gives him a look of understanding.

“I’m glad one of you have the decency to apologize properly.”

“Properly…?” Bruce asks in confusion. Rhodey hums and hands him the letter that was sent to Tony. Bruce blinks and begins to read it. As he read it, the green around his irises began to grow. “What the fuck is this?”

“An ‘Apology Letter’ from Rogers.” Rhodey responds easily. “To Tony.”

“This isn’t a damn apology.”

“Agreed. How’s the surgery going?” Rhodey swerves the conversation as Bruce’s fingertips start turning green. Bruce sighs as the green recedes from the outside.

“We have to use Extremis or else he won’t make it.” Bruce slumps in his seat. “It’s all my fault, I should have been there.”

“You left because of what Maximoff did and you were afraid. Things could have turned out differently if you were here but I get why you left.” Rhodey explains. “Doesn’t mean I’ll forgive you as soon as Tony will.”

“I expect nothing less. I..read the Accords. I got an agreement that they would only call me if the world was under threat..” Bruce says quietly. Rhodey looks at him with a bit of a surprise in his eyes.

“You did? Tony told me a bit about your history with Ross..”

“Tony wouldn’t let him do anything that would hurt me or the people he care about which includes enhanced individuals.. I trust him to stop Ross from making us weapons or anything like that.” Bruce admits. Rhodey snorts in amusement.

“Rogers said you would have gone against the Accords.” Bruce blinks in surprise.

“I would have probably gone into retirement more than disagreeing with them. While the Accords aren’t perfect, I can agree with most stuff and I’m sure Tony can get them amended with some help..” Bruce hums thoughtfully.

“You know, Tony should get the same agreement as you..”

“What agreement?” Rhodey and Bruce looks over to see Tony walking out of the surgery room looking a lot healthier and younger.

“Dr. Banner here got an agreement with the Council as to not call him in unless the world was in danger. I was saying that you should get something similar. There are enough enhanced people around the world that can handle New York or the entire country Tones.” Rhodey tries to insist. Tony looks thoughtful about the agreement.

“I’ll think about it...It would give me more time for the company schematics and for charity events.” Tony hums.

“And more time for yourself to just build what you like, read, pick up another hobby..” Bruce offers.

“I have been wanting to pick up cooking again..” Tony mumbles. “I’ll think about it.” He declares. Bruce and Rhodey share a conspiratory smile.

“Of course Tones.”

“Sure thing Tony.” Tony eyes them warily but smiles brightly.

“Let’s head back to the tower! I want to see what we can do about the Compound.” Tony walks to the car with Bruce and Rhodey trailing behind him.

“I may have a suggestion..” Bruce starts hesitantly. Tony hums in acknowledgement. “Maybe we can make it a school for those that are enhanced but don’t want to be too far from home?”

“I knew I loved you for more than your looks Brucie bear! I’ll talk to Charles and Stephen to see what we can do!” Tony grins at him. Bruce gets a bit flustered but smiles.

“I’m with you all the way Tones. It’s also quite good revenge on the Rouges.”

“You are being petty Honeybear.”

“One of us have to be.”


	3. Year 1

**Summary for the Chapter:**

> I'm mainly going to put the first year of Bruce reintegrating himself in Tony's life, this will include some Science Bros (platonic at first), gay realization (On Bruce's part), Peter Parker basic adoption, Harley Keener and his sister's basic adoption, and saving the Barton Family. I'll do a chapter on the Rogues next

Bruce was working on the chemical makeup of the super soldier system to make a drug to knock out a super soldier if the need arises. He was back at Stark Tower and Tony was gracious enough to allow him to have his floor and lab back. He would never be more grateful to him. As he worked in silence his mind wandered onto the effects of Extremis. Tony mentioned that he suddenly had an influx of information which, according to FRIDAY, was the internet. He was kind of worried about all that information going through Tony’s head. After a few days, however, Tony was back to his old self commenting that he had gotten control of the information with FRIDAY’s help.

“Dr. Banner, you have been working for a total of 56 hours. I insist you get some rest.” FRIDAY comments. Bruce waves her warning off. He was startled when Tony bursts into his lab.

“Brucie bear! If I can't work for more than 32 hours neither can you!” Tony smirks. Bruce rolls his eyes in fond exasperation.

“Tony, I’m almost done-” Bruce doesn’t get the chance to finish as Tony pouts at him.

“Come onnnn let’s go watch some sci-fi movies and trash the science there!” Tony grins. Bruce sighs dramatically.

“You know my weakness.” Bruce chuckles as he gets up. Tony cheers and heads back to the elevator with Bruce following.

They arrive at the common room and Bruce make a beeline for the kitchen first. “Gonna make some coffee while we watch?” Bruce calls back to Tony.

“Ooh yes please!” Tony arrives in the kitchen soon after Bruce has spoken. There was a comfortable silence between the two as they made their respective drinks. Tea for Bruce and Coffee (Nectar of the Gods) for Tony. “Horrid leaf juice.” He huffs squinting at Bruce’s cup. Bruce chuckles and smiles at the other scientist.

“It’s healthy.”

“ _Horrid_.” Tony insists making Bruce laugh a bit. They migrate to the couch in the common room, each of them leaning on the opposite side of the couch. “FRIDAY, turn on my science watchlist please sweetheart?”

“Of course Boss.” The lights dim and the movies begin. The two were found by Rhodey later leaning against each other asleep.

A month later, Tony was working on designs for new prosthetics for when he shows Pepper his idea about SI going into the medical field. As he was putting the finishing touches on the design Bruce came in. Bruce silently looks over his shoulder and marvels at the design. “Well? What do you think?”

“I’m very impressed and amazed Tony.” Bruce says with awe in his voice. “How long did you spend on this?”

“A couple of months, after I finished Honey-bear’s legs. I got the idea that maybe SI could go into the medical field. We could make a killing when it comes to prosthetics! When I submit these designs we can mass produce them and they could be cheaper for people that can’t buy them normally!. Think about the possibilities Bruce! With more people able to get prosthetics we would also be helping Physical Therapy Instructors and Centers help more people and all those _kids_ won’t feel left out or even different!” Tony started rambling. “OH! We should also find a way to make it so that they won’t feel different about having a prosthetic.. OH! What if we get some animators or even a comic book studio to make a hero that has prosthetics?! That would be so cool and will get kids to associate their prosthetic with something good! Yeah??” Tony looks at Bruce, his eyes sparkling with excitement, smiling widely. Bruce swallows thickly. He wasn’t expecting this but as he was listening he was amazed at all the thought put into it, even if it was on the fly.

“Wow...that’s just..that sounds amazing Tony!” Bruce finally answers. Tony’s eyes light up at the approval and Bruce could have sworn his heart skipped a beat. He ignores it to smile back at Tony.

“You hear that baby girl?! Call Pep!” Tony turns around to face his design and Bruce settles himself on the couch content with watching Tony’s bots run around while Tony talks to Pepper with excitement.

A week later, SI is introducing their new prosthetics in order to help people disabled all around the world. Tony and Rhodey went to a press conference about it. Bruce watches from the couch in Stark Tower. He couldn’t help but focus on Tony when he spoke. His cool and sharp eyes with a charming smirk.

“Mr. Stark! Mr. Stark!” One report begins to shout. Tony nods to him. “Why did you decide to make these prosthetics?" Tony allows a guilty but soft expression to appear on his face.

“During the ‘Civil War’ as the media call it, my friend Colonel Rhodes here was injured and his lower spine was permanently damaged. I felt guilty since I called him to come with me so I built him braces to help him walk again. Afterwards, I thought why not go into prosthetics and help everyone!” Tony replies with a grin.

“I keep telling him that he had nothing to feel guilty about, we weren’t even expecting a fight.” Rhodey adds while throwing his arm over Tony’s shoulder making said male laugh. Bruce couldn’t help but chuckles. You could always count on Rhodey to ease tension.  
Soon enough, they had return to the Tower along with another, younger, individual. Bruce greets them as they walk inside.

“Oh my god!” Peter gasps. Bruce winces, it’s not unusual for people to be excited about the other guy.

“You’re Bruce Banner, you have like 7 PhDs and I have a poster of you! My wig has been snatched. Oh my gods.” Peter starts rambling as Bruce stares. He then makes eye contact with Tony and they share a small smile.

Bruce isn’t surprised when he is pulled out of his lab by an excitable spider child for dinner or movies. He is surprised when he’s dragged to Tony’s lab and is quite amused to see that Peter has been given his own part of the lab to do his own science.

Two weeks past before the next two kids of the household shows up. Tony blinks wearily as he stares at Harley and Stephanie Keener. They were standing outside the tower and looked very tired. “Oh my gods, come in you two!” He ushers them inside and takes them to the Penthouse. “Why were you two even out there? Shouldn’t you be with your mother?” Harley smiles sheepishly.

“Yeah..about that..” Harley hands him a letter and Tony accepts it. He absentmindedly leads the kids inside as he read the letter. Turns out their mother needed them to be in a stable home while she finds a job to make a living. Tony idly remembers the state of their home when he first arrived their and thought it was wise of her to do so. Tony sighs fondly before looking at the two.

“Alright, looks like you’ll be staying here for an indefinite amount of time. I’m guessing your mother would refuse any money I try to give her so I’ll have to talk to her about a compromise.” He chuckles as their eyes widened. “First things first let’s set up your rooms then introductions!” Tony claps before leading them towards the rooms.

Peter and Harley immediately hit it off and begins talking about Harley’s Potato gun and what modifications could be made. Stephanie was content with watching cartoons on the TV. Tony watches the three with fond exasperation before Bruce walks in. “Jolly Green! You finally crawled out of your lab!” Tony smirks as Bruce heads into the kitchen.

“I’m surprised you’re not _in_ your lab.” Tony gasps dramatically before motioning to the three young ones in the room.

“As you can see Green Giant, I have to watch Underoos, Hotshot, and Sparkle over here!” Peter groans at the nickname while Harley snickers.

“Now Sparkle don’t laugh at Underoos.” Harley fakes a look of offense. Bruce laughs and returns to the group with a cup of tea. Tony spots in and squints at it. “Horrid Leaf Juice.”

“It’s Healthy.”

“ _Horrid_.” Tony sniffs dispassionately before turning back to Peter and Harley. Bruce watches him as his eyes soften. Tony begins to chat with the two science kids and Bruce can’t help but notice the small features in Tony’s face. The slight dimples, the curve of his eyes, how they brighten a shade when he’s excited. Bruce tears his gaze away his face dusted with pink.

That night, Bruce finds himself watching an action film with Harley, Tony, Peter, and Stephanie. Rhodey, Pepper, and Happy ends up joining as well.

A week later, Bruce wakes up to Peter curled up into his side and Harley sprawled over him and Tony. Stephanie curled up into Tony’s free side and Tony was leaning against him.

Only a few months later, things got a little bad. “Ross will probably send a kill squad to Clint’s family…” Tony bites his lip pacing nervously. “I have to go and help-”

“Tony.. you don’t have to go.” Bruce says slowly Tony opens his mouth to retort. “Rhodey can go, and so can the Avengers Initiative. _You_ don’t have to go.”

“Y-you’re right. I-I just have to know if they’re okay.”

“Ross is probably watching your every move at this point. Why not send someone else so that he won’t know and have them brought here secretly?” Bruce offers. Tony looks at him with a timid smile and Bruce couldn’t help the warm feeling that came over him.

“Yeah. That works great! Thanks Bruce.” Tony grins. Bruce smiles and nods.

That afternoon, Laura Barton arrives with Nathaniel, Lila, and Cooper. They are given a floor in the tower. They refused to move into Clint’s old floor.

That night, Bruce and Tony was in the kitchen drinking their respective drinks. “Boss, Dr. Banner, you have been up for 38 hours. I insist you get some rest.” Tony sighs but grins.

“Sure thing cupcake.” Tony responds before passing Bruce with a pat on the shoulder. Bruce smiles softly and nods at him before heading to his room.

That night was when Tony began to trust him again.


End file.
